I have a problem with cleaning my protein before ligand docking. I use the command clean_pdb.py 1i09 A to download and clean GSK-3, but the final structure has some missing residues, even more than the initial structure in the protein data bank. There is no gap in the AA sequence when open the structure as a text file, but using PyMol, there are dotted lines instead of solid lines in some areas of the structure. I have uploaded the initial and the cleaned PDB files for your consideration.
Also, how should I determine if I need to relax the protein before docking or not?
I have one more question regarding the double bonds in ligand PDB files. When using mole_to_params.py, all the double bonds in the SDF file turn into single bonds in the PDB file. I used Open Babel to keep the double bonds, but when I place the ligand into the binding site, they disappear again. I see that in the material given in the Rosetta virtual workshop (2020) all the double bonds are present in PDB files. I was wondering if that makes a problem in the docking process.
|The protein structure obtained from protein data bank||489.64 KB|
|The protein structure after using clean_pdb.py 1i09 A||206.22 KB|